On Tue, Nov 08, 2016, Vladislav Sláma wrote:
>
> I have tried comparing energies and here are the results:
> For initial configuration I receive from NAB:
>
> iter Total bad vdW elect nonpolar genBorn
> frms
> ff: 0 113013.79 4458.86 108611.29 -56.37 0.00 0.00
> 5.38e+03
>
> and from sander:
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 4.9198E+03 1.7964E+01 7.5305E+01 C90 90
>
> BOND = 193.1278 ANGLE = 3623.6104 DIHED = 642.1252
> VDWAALS = 290.9881 EEL = 60.9590 HBOND = 0.0000
> 1-4 VDW = 226.0755 1-4 EEL = -117.0890 RESTRAINT = 0.0000
>
> I think that there is something
> wrong with my NAB input files or NAB reads bonds from prmtop file
> somehow differently than sander.
(I thought I had answered this earlier....) The results above show that the
bond-angle-dihedral energy is identical in NAB and sander. So this almost
certainly has nothing to do with how NAB reads bonds from the prmtop file.
The difference is entirely in the vdW terms with the NAB energy being much
higher than the sander result. Is there anything unusual about how you
created the prmtop file? Have you tried a similar comparison using residues
that are in the standard libraries? We have tests of exactly this sort of
comparison in the Amber test suite, so there is something unusal about your
specific situation. Any clues you can provide about anything "non-standard"
that you did might help in debugging.
...dac
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Received on Tue Nov 08 2016 - 12:30:03 PST
